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OPENSEQ.org
cI_F_cIII_cyt1_10
Genes: A B A+B
Length: 184 263 424
Sequences: 2037 884 276
Seq/Len: 11.07 3.36 0.65
MirrorTree (Pazo et al. 2001) 0.45
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.00 0.01 0.00
2 0.00 0.01 0.00
5 0.00 0.01 0.00
10 0.00 0.01 0.00
20 0.00 0.01 0.01
100 0.01 0.01 0.05
∞ 0.02 0.01 0.62
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results (Scaled_score > 1):
Figure 4: The darker and larger the blue dots, the higher strength in coevolution. 		Inter Residue pairs sorted by strength in coevolution signal:
i j Scaled Score Prob I_Prob
52_G 157_V 1.50 0.64 0.00
22_H 250_K 1.35 0.53 0.00
21_T 254_Q 1.30 0.48 0.00
11_I 256_I 1.17 0.38 0.00
170_N 241_L 1.16 0.37 0.00
129_V 149_G 1.14 0.35 0.00
163_R 80_L 1.13 0.34 0.00
165_G 229_Q 1.10 0.32 0.00
107_I 101_E 1.09 0.32 0.00
37_L 116_G 1.08 0.31 0.00
138_V 241_L 1.07 0.30 0.00
20_I 235_V 1.06 0.30 0.00
15_A 191_S 1.05 0.29 0.00
98_I 157_V 1.05 0.29 0.00
107_I 93_D 1.05 0.29 0.00
92_V 215_F 1.04 0.28 0.00
181_E 63_G 1.04 0.28 0.00
170_N 44_Q 1.03 0.28 0.00
16_T 100_E 1.03 0.28 0.00
21_T 131_A 1.03 0.28 0.00
89_K 215_F 1.03 0.28 0.00
40_S 46_Q 1.03 0.27 0.00
57_I 139_T 1.02 0.27 0.00
126_A 105_R 1.02 0.27 0.00
85_R 230_V 1.01 0.26 0.00
147_L 44_Q 1.01 0.26 0.00
40_S 135_G 1.01 0.26 0.00
92_V 194_Q 1.00 0.26 0.00
20_I 55_T 1.00 0.26 0.00
153_V 87_A 0.99 0.25 0.00
9_G 158_L 0.99 0.25 0.00
51_A 143_Q 0.98 0.24 0.00
134_F 157_V 0.98 0.24 0.00
144_A 206_D 0.98 0.24 0.00
102_I 88_Y 0.97 0.24 0.00
169_S 207_Q 0.97 0.24 0.00
89_K 221_E 0.97 0.23 0.00
57_I 154_I 0.96 0.23 0.00
102_I 93_D 0.96 0.23 0.00
15_A 236_I 0.96 0.23 0.00
133_L 125_L 0.96 0.23 0.00
143_L 143_Q 0.95 0.23 0.00
179_K 49_R 0.95 0.23 0.00
35_S 210_T 0.95 0.23 0.00
153_V 53_V 0.94 0.22 0.00
86_Q 154_I 0.94 0.22 0.00
129_V 84_Q 0.94 0.22 0.00
160_R 104_P 0.93 0.21 0.00
21_T 93_D 0.93 0.21 0.00
97_A 246_Y 0.92 0.21 0.00
47_G 49_R 0.92 0.21 0.00
22_H 218_W 0.92 0.21 0.00
98_I 214_A 0.92 0.21 0.00
141_V 136_P 0.92 0.21 0.00
163_R 69_L 0.91 0.21 0.00
117_Q 94_I 0.91 0.20 0.00
112_L 39_F 0.91 0.20 0.00
130_G 220_A 0.91 0.20 0.00
29_L 136_P 0.91 0.20 0.00
56_I 225_M 0.91 0.20 0.00
126_A 236_I 0.90 0.20 0.00
13_I 133_F 0.90 0.20 0.00
45_S 82_E 0.90 0.20 0.00
152_L 43_D 0.90 0.20 0.00
20_I 224_M 0.90 0.20 0.00
41_G 76_G 0.90 0.20 0.00
153_V 188_A 0.89 0.20 0.00
35_S 151_P 0.89 0.20 0.00
46_L 23_H 0.89 0.19 0.00
145_S 219_T 0.89 0.19 0.00
165_G 249_N 0.89 0.19 0.00
20_I 182_N 0.89 0.19 0.00
79_S 214_A 0.89 0.19 0.00
120_D 81_P 0.89 0.19 0.00
152_L 90_A 0.89 0.19 0.00
147_L 81_P 0.89 0.19 0.00
153_V 201_T 0.89 0.19 0.00
172_K 182_N 0.89 0.19 0.00
131_I 254_Q 0.88 0.19 0.00
93_W 149_G 0.88 0.19 0.00
83_Q 130_R 0.88 0.19 0.00
19_V 219_T 0.88 0.19 0.00
10_L 90_A 0.88 0.19 0.00
39_I 218_W 0.88 0.19 0.00
156_F 224_M 0.88 0.19 0.00
22_H 72_L 0.88 0.19 0.00
138_V 65_R 0.87 0.18 0.00
147_L 224_M 0.87 0.18 0.00
10_L 74_D 0.87 0.18 0.00
134_F 197_Y 0.86 0.18 0.00
178_R 105_R 0.86 0.18 0.00
99_L 213_A 0.86 0.18 0.00
152_L 244_L 0.86 0.18 0.00
97_A 106_V 0.86 0.18 0.00
44_F 249_N 0.86 0.18 0.00
167_V 127_A 0.86 0.18 0.00
144_A 194_Q 0.86 0.18 0.00
99_L 236_I 0.85 0.18 0.00
10_L 151_P 0.85 0.17 0.00
104_L 240_V 0.85 0.17 0.00
101_A 214_A 0.85 0.17 0.00
76_L 221_E 0.84 0.17 0.00
98_I 91_N 0.84 0.17 0.00
4_A 223_K 0.84 0.17 0.00
53_A 215_F 0.84 0.17 0.00
143_L 137_Y 0.84 0.17 0.00
50_F 102_D 0.84 0.17 0.00
165_G 239_I 0.84 0.17 0.00
143_L 256_I 0.84 0.17 0.00
29_L 82_E 0.84 0.17 0.00
77_G 43_D 0.84 0.17 0.00
103_M 241_L 0.83 0.17 0.00
121_G 125_L 0.83 0.17 0.00
126_A 93_D 0.83 0.17 0.00
107_I 88_Y 0.83 0.17 0.00
78_G 213_A 0.83 0.17 0.00
124_I 130_R 0.83 0.17 0.00
28_A 215_F 0.83 0.16 0.00
144_A 99_T 0.83 0.16 0.00
40_S 49_R 0.83 0.16 0.00
167_V 125_L 0.83 0.16 0.00
13_I 91_N 0.83 0.16 0.00
127_K 74_D 0.82 0.16 0.00
41_G 41_K 0.82 0.16 0.00
173_D 41_K 0.82 0.16 0.00
29_L 176_N 0.82 0.16 0.00
37_L 144_L 0.82 0.16 0.00
37_L 115_S 0.82 0.16 0.00
109_Y 90_A 0.81 0.16 0.00
136_P 131_A 0.81 0.16 0.00
88_L 242_A 0.81 0.15 0.00
142_E 135_G 0.81 0.15 0.00
78_G 214_A 0.81 0.15 0.00
99_L 114_V 0.81 0.15 0.00
146_M 126_M 0.81 0.15 0.00
60_A 238_L 0.81 0.15 0.00
11_I 111_F 0.81 0.15 0.00
17_L 176_N 0.81 0.15 0.00
177_K 200_G 0.81 0.15 0.00
168_L 96_D 0.80 0.15 0.00
82_E 165_E 0.80 0.15 0.00
Figure 5: The i (protein A) and j (protein B) are positions as given in the query sequences.

Scaled Score = raw_score/average(raw_scores)
Prob = P(contact | scaled_score, seq/len)
I_Prob = P(contact | scaled_score, seq/len, top_inter_score)
ID Seq/Len Name Options I_Prob Status
2421 0.65 cI_F_cIII_cyt1_10 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) 0.00 Done - Shared
2293 0.41 cI_F_cIII_cyt1 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) 0.03 Done - Shared
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